The U.S. government labeled a prominent journalist as a member of Al Qaeda and placed him on a watch list of suspected terrorists, according to a top-secret document that details U.S. intelligence efforts to track Al Qaeda couriers by analyzing metadata.

The briefing singles out Ahmad Muaffaq Zaidan, Al Jazeera’s longtime Islamabad bureau chief, as a member of the terrorist group. A Syrian national, Zaidan has focused his reporting throughout his career on the Taliban and Al Qaeda, and has conducted several high-profile interviews with senior Al Qaeda leaders, including Osama bin Laden.

A slide dated June 2012 from a National Security Agency PowerPoint presentation bears his photo, name, and a terror watch list identification number, and labels him a “member of Al-Qa’ida” as well as the Muslim Brotherhood. It also notes that he “works for Al Jazeera.”

The presentation was among the documents provided by NSA whistleblower Edward Snowden.

In a brief phone interview with The Intercept, Zaidan “absolutely” denied that he is a member of Al Qaeda or the Muslim Brotherhood. In a statement provided through Al Jazeera, Zaidan noted that his career has spanned many years of dangerous work in Afghanistan and Pakistan, and required interviewing key people in the region — a normal part of any journalist’s job.

“For us to be able to inform the world, we have to be able to freely contact relevant figures in the public discourse, speak with people on the ground, and gather critical information. Any hint of government surveillance that hinders this process is a violation of press freedom and harms the public’s right to know,” he wrote. “To assert that myself, or any journalist, has any affiliation with any group on account of their contact book, phone call logs, or sources is an absurd distortion of the truth and a complete violation of the profession of journalism.”

A spokesman for Al Jazeera, a global news service funded by the government of Qatar, cited a long list of instances in which its journalists have been targeted by governments on which it reports, and described the labeling and surveillance of Zaidan as “yet another attempt at using questionable techniques to target our journalists, and in doing so, enforce a gross breach of press freedom.”

The document cites Zaidan as an example to demonstrate the powers of SKYNET, a program that analyzes location and communication data (or “metadata”) from bulk call records in order to detect suspicious patterns.

In the Terminator movies, SKYNET is a self-aware military computer system that launches a nuclear war to exterminate the human race, and then systematically kills the survivors.

According to the presentation, the NSA uses its version of SKYNET to identify people that it believes move like couriers used by Al Qaeda’s senior leadership. The program assessed Zaidan as a likely match, which raises troubling questions about the U.S. government’s method of identifying terrorist targets based on metadata.

It appears, however, that Zaidan had already been identified as an Al Qaeda member before he showed up on SKYNET’s radar. That he was already assigned a watch list number would seem to indicate that the government had a prior intelligence file on him. The Terrorist Identities Datamart Environment, or TIDE, is a U.S. government database of over one million names suspected of a connection to terrorism, which is shared across the U.S. intelligence community.

The presentation contains no evidence to explain the designation.

Peter Bergen, CNN’s national security analyst and author of several books on Al Qaeda and Osama bin Laden, told The Intercept, “I’ve known [Zaidan] for well over a decade, and he’s a first class journalist.”

“He has the contacts and the access that of course no Western journalist has,” said Bergen. “But by that standard any journalist who spent time with Al Qaeda would be suspect.” Bergen himself interviewed bin Laden in 1997.

The NSA and the Office of the Director of National Intelligence declined to answer questions about the basis of Zaidan’s inclusion on the watch list and alleged Al Qaeda affiliation. The NSA also declined to answer a set of detailed questions about SKYNET, and how it uses the information about the people that it identifies.

What is clear from the presentation is that in the NSA’s eyes, Zaidan’s movements and calls mirrored those of known Al Qaeda couriers.

According to another 2012 presentation describing SKYNET, the program looks for terrorist connections based on questions such as “who has traveled from Peshawar to Faisalabad or Lahore (and back) in the past month? Who does the traveler call when he arrives?” and behaviors such as “excessive SIM or handset swapping,” “incoming calls only,” “visits to airports,” and “overnight trips.”

That presentation states that the call data is acquired from major Pakistani telecom providers, though it does not specify the technical means by which the data is obtained.

The June 2012 document poses the question: “Given a handful of courier selectors, can we find others that ‘behave similarly’” by analyzing cell phone metadata? “We are looking for different people using phones in similar ways,” the presentation continues, and measuring “pattern of life, social network, and travel behavior.”

For the experiment, the analysts fed 55 million cell phone records from Pakistan into the system, the document states.

The results identified someone who is “PROB” — which appears to mean probably — Zaidan as the “highest scoring selector” traveling between Peshawar and Lahore.

The following slide appears to show other top hits, noting that 21 of the top 500 were previously tasked for surveillance, indicating that the program is “on the right track” to finding people of interest. A portion of that list visible on the slide includes individuals supposedly affiliated with Al Qaeda and the Taliban, as well as members of Pakistan’s spy agency, Inter-Services Intelligence. But sometimes the descriptions are vague. One selector is identified simply as “Sikh Extremist.”

As other documents from Snowden revealed, drone targets are often identified in part based on metadata analysis and cell phone tracking. Former NSA director Michael Hayden famously put it more bluntly in May 2014, when he said, “we kill people based on metadata.”

Metadata also played a key role in locating and killing Osama bin Laden. The CIA used cell phone calling patterns to track an Al Qaeda courier and identify bin Laden’s hiding place in Pakistan.

Yet U.S. drone strikes have killed many hundreds of civilians and unidentified alleged “militants” who may have been marked based on the patterns their cell phones gave up.

People whose work requires contact with extremists and groups that the U.S. government regards as terrorists have long worried that they themselves could look suspicious in metadata analysis.

“Prominent American journalists have interviewed members of blacklisted terrorist groups, including Al Qaeda,” said Jameel Jaffer, deputy legal director of the American Civil Liberties Union. “It would surprise me if journalists in Pakistan hadn’t done the same. Part of the job of journalists and human rights advocates is to talk to people the government doesn’t want them to talk to.”

A History of Targeting Al Jazeera

The U.S. government’s surveillance of Zaidan is not the first time that it has linked Al Jazeera or its personnel to Al Qaeda.

During the invasion of Afghanistan, in November 2001, the United States bombed the network’s Kabul offices. The Pentagon claimed that it was “a known al-Qaeda facility.”

That was just the beginning. Sami al-Hajj, an Al Jazeera cameraman, was imprisoned by the U.S. government at Guantanamo for six years before being released in 2008 without ever being charged. He has said he was repeatedly interrogated about Al Jazeera. In 2003, Al Jazeera’s financial reporters were barred from the trading floor of the New York Stock Exchange for “security reasons.” Nasdaq soon followed suit.

During the invasion of Iraq, U.S. forces bombed Al Jazeera’s Baghdad offices, killing correspondent Tariq Ayoub. The U.S. insisted it was unintentional, though Al Jazeera had given the Pentagon the coordinates of the building. When American forces laid siege to Fallujah, and Al Jazeera was one of the few news organizations broadcasting from within the city, Bush administration officials accused it of airing propaganda and lies. Al Jazeera’s Fallujah correspondent, Ahmed Mansour, reported that his crew had been targeted with tanks, and the house they had stayed in had been bombed by fighter jets.

So great was the suspicion of Al Jazeera’s ties to terrorism that Dennis Montgomery, a contractor who had previously tried peddling cheat-detector software to Las Vegas casinos, managed to convince the CIA that he could decode secret Al Qaeda messages from Al Jazeera broadcasts. Those “codes” reportedly caused Bush to ground a number of commercial transatlantic flights in December 2003.

But the U.S. government appeared to have somewhat softened its view of the network in the last several years. The Obama administration has criticized Egypt for holding three of Al Jazeera’s journalists on charges of aiding the Muslim Brotherhood. During the height of the 2011 Arab Spring, then-Secretary of State Hillary Clinton praised the network’s coverage, saying, “Viewership of Al Jazeera is going up in the United States because it’s real news.”

A Journalist and Al Qaeda

Zaidan first came to international prominence after the 9/11 attacks because of his access to senior Al Qaeda leadership. Zaidan wrote an Arabic-language book on bin Laden, and interviewed him in person multiple times.

“He covered the wedding of bin Laden’s son which was shortly after the [U.S.S.] Cole attack, and I think it was a very useful piece of journalism, because bin Laden declaimed a poem about the Cole which implied him taking responsibility for the attacks, which of course he later did,” said Bergen.

Zaidan also received a number of bin Laden’s taped messages to Americans, which were broadcast on Al Jazeera.

In 2002, he met a mysterious man with a “half-covered face,” who handed him a cassette tape with bin Laden’s voice, Zaidan told Bergen in an interview. In 2004, another bin Laden tape was dropped off at the office gate, Zaidan told the Associated Press. “The guard brought it to me along with other mail. It was in an envelope, I opened it and it was a big scoop,” Zaidan recounted.

Zaidan, right, in a 2011 Al Jazeera documentary he made about bin Laden.

Files collected from bin Laden’s Abbottabad compound after his death — a portion of which were released this year — indicate that Al Qaeda members viewed Zaidan as a journalist they felt comfortable dealing with.

In an August 2010 missive, discussing Zaidan’s plans for a documentary, bin Laden directs his deputies to get “brother Ahmad Zaydan’s” questions and “tell him it would be good if it was on the tenth anniversary of September Eleventh.” Any other input should come in “an indirect way,” bin Laden cautions. “If we want this program to be a success, then we should not get involved in the details of how it is run, except that I don’t want him to interview any of my family,” he wrote.

Zaidan released his documentary on Al Jazeera in December 2011, an oral history of bin Laden’s years in Pakistan and Afghanistan comprised of interviews with a range of people who had known him, including Taliban fighters, government officials, and many journalists.

Bin Laden had also grown paranoid about meetings with Zaidan, although he did not think the U.S. government had managed to kill anyone “from surveying Ahmad Zaydan,” he wrote in May 2010.

He continued, “keep in mind, the possibility, though remote, that the journalists may be involuntarily monitored in a way that we or they do not know about, either on ground or by satellite, especially Ahmad Zaydan of Al Jazeera, and it is possible that a tracking chip could be put into some of their personal effects before coming to the meeting place.”

Zaidan is still Al Jazeera’s Islamabad bureau chief, and has also reported from Syria and Yemen in recent years. Al Jazeera vigorously defended his reporting. “Our commitment to our audiences is to gain access to authentic, raw, unfiltered information from key sources and present it in an honest and responsible way.” They added that, “our journalists continue to be targeted and stigmatized by governments,” even though “Al Jazeera is not the first channel that has met with controversial figures such as bin Laden and others — prominent western media outlets were among the first to do so.”

Disclosure: As freelancers, Cora Currier wrote an article for Al Jazeera America and Andrew Fishman field produced segments for Al Jazeera English’s “The Listening Post.” Glenn Greenwald was a paid studio guest of Al Jazeera’s in Doha on the night of the 2012 U.S. presidential election.